Phelan replaces Ruth Crawford, who was based in the US and quit GSK in June.
Phelan continues to be based in Greenford, west London, in GSK's global commercial strategy group.
Her promotion is believed to have been announced internally last week. She is now looking for a replacement in her former position of product PR director.
GSK is seen as having one of the industry's strongest drug pipelines, having transformed its research labs in recent years.